As per Honda EU 2000i Specs:
120V 2000W max. (16.7A) 1600W rated (13.3A)
d The "rated" is continuous output.
The Honda EU 1000i specs:
120V 1000W max. (8.3A) 900W rated (7.5A)
I have no idea where you are getting the "charger output of 40 amps" from a EU 2000I, or 20 amps from a EU 1000i. But I run a West Marine branded, portable battery charger, output (measured with external amp meter) of slightly over 30 amps, plus other light loads. (Charging 2 AGM group 31 110 amp hour batteries) The EU 1000 will not run the Mastervolt 20 amp, plus the Torqeedo charger, plus the 30 amp output. However by the time the 30 amp charger is down to about 20 amps, the EU 1000 will run all 3. (which would be about 7.5 amps at 110 volts.)
My documented experience says that your "calculations" are not correct. Yes, some battery chargers are more efficient than others.
Lets take this to the theoretical level: The most efficient battery chargers will put out 85% of the input amperage: Assume that the Honda is putting out 120 volts, and the battery charger is putting out 12 volts (reality is that the battery charger is putting out 14.3 volts at 30 amps). This means that there is a factor of 10:1, or 7.5 amps of 120 V = 75 amps at 12 V : 85% of that would be 63.75 amps or the theoretical 12 volt out put of max current production of the EU1000..
Since the true battery voltage is 14.3 at output, solving the equation shows that theoretical max output at 14.3 volts would be 53.5 amps of 12 volt DC. Not 20 as stated.
Unfortunately the Guest chargers supplied with our boats are not the most efficient chargers. My experience is that they only last a few years, especially in regular use. This is the reason I have had to replace every Guest charger that has come with my C Dorys. This is often the case with production boats. The custom and more expensive boats often come with a higher quality charger--such as Victron, Blue Seas, VMI (Macaroon) or MasterVolt. These are far more expensive, and generally are far more reliable as well as being more efficient. They are also programable for different type of batteries, and some being able to independently charge each battery to its best perimeters.